This study investigated alterations in heart rate variability (HRV) and cognitive performance before and after physical effort, for 30 high-level track and field athletes (23 males and 7 females). Interbeat intervals were assessed at the baseline and during each task of a CogState cognitive battery (simple reaction time, choice reaction time, working memory, short-term memory and sustained attention). Time and frequency domain measures of HRV were compared between conditions and between tasks. The results indicated differences in HRV between executive and non-executive tasks. There was a significant increase in sympathetic-modulation-related indices after physical effort. The differences between executive and non-executive tasks were the same in post-test. Correlations were found between HRV and cognitive performance, which differed by speed and accuracy. We conclude that HRV is related to cognitive demand and that the correlation between HRV and cognitive performance seems to be stronger after physical exercise. The results raise questions about the psychophysiological meaning of different HRV signals and this has implications for future research about the relationship between HRV and cognition.